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<i>Bordetella bronchiseptica</i> infections may be overlooked by clinicians due to the uncommon encounter of this pathogen in humans and common isolation of co-pathogens. However, the isolation of <i>B. bronchiseptica</i> in immunocompromised individuals may represent a true infection. We report our experience with the fatal case of a stem cell transplant recipient, co-infected with SARS-CoV-2 and <i>B. bronchiseptica</i>, who was considered fully vaccinated (two doses) at the time of her case in spring 2021. Future studies are needed to evaluate the incidence of bacterial co-infections in immunosuppressed individuals with SARS-CoV-2 and clinicians should remain cognizant of the potential pathogenic role of uncommon pathogens isolated in these individuals.